1
|
Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
Collapse
Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| |
Collapse
|
2
|
Hasan M, Patel D, Ellis N, Brown SP, Lewandowski JR, Dixon AM. Modulation of Transmembrane Domain Interactions in Neu Receptor Tyrosine Kinase by Membrane Fluidity and Cholesterol. J Membr Biol 2019; 252:357-369. [DOI: 10.1007/s00232-019-00075-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/09/2019] [Indexed: 01/06/2023]
|
3
|
Nami B, Maadi H, Wang Z. The Effects of Pertuzumab and Its Combination with Trastuzumab on HER2 Homodimerization and Phosphorylation. Cancers (Basel) 2019; 11:cancers11030375. [PMID: 30884851 PMCID: PMC6468664 DOI: 10.3390/cancers11030375] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 01/18/2023] Open
Abstract
Pertuzumab (Perjeta) is an anti-HER2 monoclonal antibody that is used for treatment of HER2-positive breast cancers in combination with trastuzumab (Herceptin) and docetaxel and showed promising clinical outcomes. Pertuzumab is suggested to block heterodimerization of HER2 with EGFR and HER3 that abolishes canonical function of HER2. However, evidence on the exact mode of action of pertuzumab in homodimerization of HER2 are limited. In this study, we investigated the effect of pertuzumab and its combination with trastuzumab on HER2 homodimerization, phosphorylation and whole gene expression profile in Chinese hamster ovary (CHO) cells stably overexpressing human HER2 (CHO-K6). CHO-K6 cells were treated with pertuzumab, trastuzumab, and their combination, and then HER2 homodimerization and phosphorylation at seven pY sites were investigated. The effects of the monoclonal antibodies on whole gene expression and the expression of cell cycle stages, apoptosis, autophagy, and necrosis were studied by cDNA microarray. Results showed that pertuzumab had no significant effect on HER2 homodimerization, however, trastuzumab increased HER2 homodimerization. Interestingly, pertuzumab increased HER2 phosphorylation at Y1127, Y1139, and Y1196 residues, while trastuzumab increased HER2 phosphorylation at Y1196. More surprisingly, combination of pertuzumab and trastuzumab blocked the phosphorylation of Y1005 and Y1127 of HER2. Our results also showed that pertuzumab, but not trastuzumab, abrogated the effect of HER2 overexpression on cell cycle in particular G1/S transition, G2/M transition, and M phase, whereas trastuzumab abolished the inhibitory effect of HER2 on apoptosis. Our findings confirm that pertuzumab is unable to inhibit HER2 homodimerization but induces HER2 phosphorylation at some pY sites that abolishes HER2 effects on cell cycle progress. These data suggest that the clinical effects of pertuzumab may mostly through the inhibition of HER2 heterodimers, rather than HER2 homodimers and that pertuzumab binding to HER2 may inhibit non-canonical HER2 activation and function in non-HER-mediated and dimerization-independent pathway(s).
Collapse
Affiliation(s)
- Babak Nami
- Department of Medical Genetics and Signal Transduction Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
| | - Hamid Maadi
- Department of Medical Genetics and Signal Transduction Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
| | - Zhixiang Wang
- Department of Medical Genetics and Signal Transduction Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
| |
Collapse
|
4
|
Abstract
Fourier transform infrared (FTIR) spectroscopy has become one of the major techniques of structural characterization of proteins, peptides, and protein-membrane interactions. While the method does not have the capability of providing the precise, atomic-resolution molecular structure, it is exquisitely sensitive to conformational changes occurring in proteins upon functional transitions or intermolecular interactions. The sensitivity of vibrational frequencies to atomic masses has led to development of "isotope-edited" FTIR spectroscopy, where structural effects in two proteins, one unlabeled and the other labeled with a heavier stable isotope, such as 13C, are resolved simultaneously based on spectral downshift (separation) of the amide I band of the labeled protein. The same isotope effect is used to identify site-specific conformational changes in proteins by site-directed or segmental isotope labeling. Negligible light scattering in the infrared region provides an opportunity to study intermolecular interactions between large protein complexes, interactions of proteins and peptides with lipid vesicles, or protein-nucleic acid interactions without light scattering problems often encountered in ultraviolet spectroscopy. Attenuated total reflection FTIR (ATR-FTIR) is a surface-sensitive version of infrared spectroscopy that has proved useful in studying membrane proteins and lipids, protein-membrane interactions, mechanisms of interfacial enzymes, the structural features of membrane pore forming proteins and peptides, and much more. The purpose of this chapter was to provide a practical guide to analyze protein structure and protein-membrane interactions by FTIR and ATR-FTIR techniques, including procedures of sample preparation, measurements, and data analysis. Basic background information on FTIR spectroscopy, as well as some relatively new developments in structural and functional characterization of proteins and peptides in lipid membranes, is also presented.
Collapse
Affiliation(s)
- Suren A Tatulian
- Department of Physics, University of Central Florida, Orlando, FL, USA.
| |
Collapse
|
5
|
Friedman R, Khalid S, Aponte-Santamaría C, Arutyunova E, Becker M, Boyd KJ, Christensen M, Coimbra JTS, Concilio S, Daday C, van Eerden FJ, Fernandes PA, Gräter F, Hakobyan D, Heuer A, Karathanou K, Keller F, Lemieux MJ, Marrink SJ, May ER, Mazumdar A, Naftalin R, Pickholz M, Piotto S, Pohl P, Quinn P, Ramos MJ, Schiøtt B, Sengupta D, Sessa L, Vanni S, Zeppelin T, Zoni V, Bondar AN, Domene C. Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology. J Membr Biol 2018; 251:609-631. [PMID: 30350011 PMCID: PMC6244758 DOI: 10.1007/s00232-018-0050-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/03/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Ran Friedman
- Department of Chemistry and Biomedical Sciences and Centre of Excellence "Biomaterials Chemistry", Linnæus University, Kalmar, Sweden.
| | - Syma Khalid
- University of Southampton, Southampton, SO17 1BJ, UK
| | - Camilo Aponte-Santamaría
- Max Planck Tandem Group in Computational Biophysics, University of Los Andes, Bogotá, Colombia.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Elena Arutyunova
- Department of Biochemistry, University of Alberta, Edmonton, Canada
| | | | - Kevin J Boyd
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Mikkel Christensen
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Interdisciplinary Nanoscience center (iNANO), Aarhus University, Aarhus, Denmark.,Sino-Danish Center for Education and Research, Beijing, China
| | - João T S Coimbra
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Simona Concilio
- Department of Industrial Engineering, University of Salerno, Fisciano, SA, Italy
| | - Csaba Daday
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | | | - Pedro A Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Frauke Gräter
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.,Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | | | | | - Konstantina Karathanou
- Department of Physics, Theoretical Molecular Biophysics Group, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | | | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Canada
| | | | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Antara Mazumdar
- GBB Institute, University of Groningen, Groningen, The Netherlands
| | - Richard Naftalin
- Physiology and Vascular Biology Departments, King's College London School of Medicine, London, UK
| | - Mónica Pickholz
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, IFIBA, Buenos Aires, Argentina
| | - Stefano Piotto
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Peter Quinn
- Biochemistry Department, King's College London, London, UK
| | - Maria J Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Interdisciplinary Nanoscience center (iNANO), Aarhus University, Aarhus, Denmark
| | - Durba Sengupta
- Physical Chemistry Division, National Chemical Laboratory, Pune, India
| | - Lucia Sessa
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Talia Zeppelin
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Valeria Zoni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Ana-Nicoleta Bondar
- Department of Physics, Theoretical Molecular Biophysics Group, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Carmen Domene
- Department of Chemistry, University of Bath, Claverton Down Bath, BA2 7AY, UK.,Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| |
Collapse
|
6
|
Exploring the dynamics and interaction of a full ErbB2 receptor and Trastuzumab-Fab antibody in a lipid bilayer model using Martini coarse-grained force field. J Comput Aided Mol Des 2014; 28:1093-107. [DOI: 10.1007/s10822-014-9787-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 08/07/2014] [Indexed: 02/01/2023]
|
7
|
Prasanna X, Praveen PJ, Sengupta D. Sequence dependent lipid-mediated effects modulate the dimerization of ErbB2 and its associative mutants. Phys Chem Chem Phys 2013; 15:19031-41. [DOI: 10.1039/c3cp52447g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
8
|
Tatulian SA. Structural characterization of membrane proteins and peptides by FTIR and ATR-FTIR spectroscopy. Methods Mol Biol 2013; 974:177-218. [PMID: 23404277 DOI: 10.1007/978-1-62703-275-9_9] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Fourier transform infrared (FTIR) spectroscopy is widely used in structural characterization of proteins or peptides. While the method does not have the capability of providing the precise, atomic-resolution molecular structure, it is exquisitely sensitive to conformational changes occurring in proteins upon functional transitions or upon intermolecular interactions. Sensitivity of vibrational frequencies to atomic masses has led to development of "isotope-edited" FTIR spectroscopy, where structural effects in two proteins, one unlabeled and the other labeled with a heavier stable isotope, such as (13)C, are resolved simultaneously based on spectral downshift (separation) of the amide I band of the labeled protein. The same isotope effect is used to identify site-specific conformational changes in proteins by site-directed or segmental isotope labeling. Negligible light scattering in the infrared region provides an opportunity to study intermolecular interactions between large protein complexes, interactions of proteins and peptides with lipid vesicles, or protein-nucleic acid interactions without light scattering problems often encountered in ultraviolet spectroscopy. Attenuated total reflection FTIR (ATR-FTIR) is a surface-sensitive version of infrared spectroscopy that has proved useful in studying membrane proteins and lipids, protein-membrane interactions, mechanisms of interfacial enzymes, and molecular architecture of membrane pore or channel forming proteins and peptides. The purpose of this article was to provide a practical guide to analyze protein structure and protein-membrane interactions by FTIR and ATR-FTIR techniques, including procedures of sample preparation, measurements, and data analysis. Basic background information on FTIR spectroscopy, as well as some relatively new developments in structural and functional characterization of proteins and peptides in lipid membranes, are also presented.
Collapse
Affiliation(s)
- Suren A Tatulian
- Department of Physics, University of Central Florida, Orlando, FL, USA.
| |
Collapse
|
9
|
Beevers AJ, Nash A, Salazar-Cancino M, Scott DJ, Notman R, Dixon AM. Effects of the Oncogenic V664E Mutation on Membrane Insertion, Structure, and Sequence-Dependent Interactions of the Neu Transmembrane Domain in Micelles and Model Membranes: An Integrated Biophysical and Simulation Study. Biochemistry 2012; 51:2558-68. [DOI: 10.1021/bi201269w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | - David J. Scott
- Department of Biosciences, University of Nottingham, Nottingham, U.K
| | | | | |
Collapse
|
10
|
Prakash A, Janosi L, Doxastakis M. GxxxG motifs, phenylalanine, and cholesterol guide the self-association of transmembrane domains of ErbB2 receptors. Biophys J 2012; 101:1949-58. [PMID: 22004749 DOI: 10.1016/j.bpj.2011.09.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 08/30/2011] [Accepted: 09/15/2011] [Indexed: 11/28/2022] Open
Abstract
GxxxG motifs are common in transmembrane domains of membrane proteins and are often introduced to artificial peptides to inhibit or promote association to stable structures. The transmembrane domain of ErbB2 presents two separate such motifs that are proposed to be connected to stability and activity of the dimer. Using molecular simulations, we show that these sequences play a critical role during the recognition stage, forming transient complexes that lead to stable dimers. In pure phospholipid bilayers association occurs by contacts formed at the C-terminus promoted by the presence of phenylalanine residues. Helices subsequently rotate to eventually pack at short separations favored by lipid entropic contributions. In contrast, at intermediate cholesterol concentrations, a different pathway is followed that involves dimers with a weaker interface toward the N-terminus. However, at high cholesterol content, a switch toward the C-terminus is observed with an overall nonmonotonic change of the dimerization affinity. This conformational switch modulated by cholesterol has important implications on the thermodynamic, structural, and kinetic characteristics of helix-helix association in lipid membranes.
Collapse
Affiliation(s)
- Anupam Prakash
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | | | | |
Collapse
|
11
|
Ng DP, Poulsen BE, Deber CM. Membrane protein misassembly in disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1115-22. [PMID: 21840297 DOI: 10.1016/j.bbamem.2011.07.046] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 07/28/2011] [Accepted: 07/29/2011] [Indexed: 11/19/2022]
Abstract
Helix-helix interactions play a central role in the folding and assembly of integral α-helical membrane proteins and are fundamentally dictated by the amino acid sequence of the TM domain. It is not surprising then that missense mutations that target these residues are often linked to disease. In this review, we focus on the molecular mechanisms through which missense mutations lead to aberrant folding and/or assembly of these proteins, and then discuss pharmacological approaches that may potentially mitigate or reverse the negative effects of these mutations. Improving our understanding of how missense mutations affect the interactions between TM α-helices will increase our capability to develop effective therapeutic approaches to counter the misassembly of these proteins and, ultimately, disease. This article is part of a Special Issue entitled: Protein Folding in Membranes.
Collapse
Affiliation(s)
- Derek P Ng
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | |
Collapse
|
12
|
Bocharov EV, Volynsky PE, Pavlov KV, Efremov RG, Arseniev AS. Structure elucidation of dimeric transmembrane domains of bitopic proteins. Cell Adh Migr 2010; 4:284-98. [PMID: 20421711 DOI: 10.4161/cam.4.2.11930] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The interaction between transmembrane helices is of great interest because it directly determines biological activity of a membrane protein. Either destroying or enhancing such interactions can result in many diseases related to dysfunction of different tissues in human body. One much studied form of membrane proteins known as bitopic protein is a dimer containing two membrane-spanning helices associating laterally. Establishing structure-function relationship as well as rational design of new types of drugs targeting membrane proteins requires precise structural information about this class of objects. At present time, to investigate spatial structure and internal dynamics of such transmembrane helical dimers, several strategies were developed based mainly on a combination of NMR spectroscopy, optical spectroscopy, protein engineering and molecular modeling. These approaches were successfully applied to homo- and heterodimeric transmembrane fragments of several bitopic proteins, which play important roles in normal and in pathological conditions of human organism.
Collapse
Affiliation(s)
- Eduard V Bocharov
- Division of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.
| | | | | | | | | |
Collapse
|
13
|
Cymer F, Schneider D. Transmembrane helix-helix interactions involved in ErbB receptor signaling. Cell Adh Migr 2010; 4:299-312. [PMID: 20212358 DOI: 10.4161/cam.4.2.11191] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Among the many transmembrane receptor classes, the receptor tyrosine kinases represent an important superfamily, involved in many cellular processes like embryogenesis, development and cell division. Deregulation and dysfunctions of these receptors can lead to various forms of cancer and other diseases. Mostly, only fragmented knowledge exists about functioning of the entire receptors, and many studies have been performed on isolated receptor domains. In this review we focus on the function of the ErbB family of receptor tyrosine kinases with a special emphasis on the role of the transmembrane domain and on the mechanisms underlying regulated and deregulated signaling. Many general aspects of ErbB receptor structure and function have been analyzed and described. All human ErbBs appear to form homo- and heterodimers within cellular membranes and the single transmembrane domain of the receptors is involved in dimerization. Additionally, only defined structures of the transmembrane helix dimer allows signaling of ErbB receptors.
Collapse
Affiliation(s)
- Florian Cymer
- Albert-Ludwigs-University Freiburg, Department of Biochemistry and Molecular Biology, ZBMZ, and Fakultät für Biologie, Freiburg, Germany
| | | |
Collapse
|
14
|
Beevers AJ, Damianoglou A, Oates J, Rodger A, Dixon AM. Sequence-Dependent Oligomerization of the Neu Transmembrane Domain Suggests Inhibition of “Conformational Switching” by an Oncogenic Mutant. Biochemistry 2010; 49:2811-20. [DOI: 10.1021/bi902087v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrew J. Beevers
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | | | - Joanne Oates
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Alison Rodger
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Ann M. Dixon
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| |
Collapse
|
15
|
Strong oligomerization behavior of PDGFβ receptor transmembrane domain and its regulation by the juxtamembrane regions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:605-15. [DOI: 10.1016/j.bbamem.2009.12.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 12/09/2009] [Accepted: 12/21/2009] [Indexed: 11/22/2022]
|
16
|
Kästner J, Loeffler HH, Roberts SK, Martin-Fernandez ML, Winn MD. Ectodomain orientation, conformational plasticity and oligomerization of ErbB1 receptors investigated by molecular dynamics. J Struct Biol 2009; 167:117-28. [DOI: 10.1016/j.jsb.2009.04.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 03/21/2009] [Accepted: 04/21/2009] [Indexed: 02/01/2023]
|
17
|
Hanshaw RG, Stahelin RV, Smith BD. Noncovalent keystone interactions controlling biomembrane structure. Chemistry 2008; 14:1690-7. [PMID: 18085538 DOI: 10.1002/chem.200701589] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There is a biomedical need to develop molecular recognition systems that selectively target the interfaces of protein and lipid aggregates in biomembranes. This is an extremely challenging problem in supramolecular chemistry because the biological membrane is a complex dynamic assembly of multifarious molecular components with local inhomogeneity. Two simplifying concepts are presented as a framework for basing molecular design strategies. The first generalization is that association of two binding partners in a biomembrane will be dominated by one type of non-covalent interaction which is referred to as the keystone interaction. Structural mutations in membrane proteins that alter the strength of this keystone interaction will likely have a major effect on biological activity and often will be associated with disease. The second generalization is to view the structure of a cell membrane as three spatial regions, that is, the polar membrane surface, the midpolar interfacial region and the non-polar membrane interior. Each region has a distinct dielectric, and the dominating keystone interaction between binding partners will be different. At the highly polar membrane surface, the keystone interactions between charged binding partners are ion-ion and ion-dipole interactions; whereas, ion-dipole and ionic hydrogen bonding are very influential at the mid-polar interfacial region. In the non-polar membrane interior, van der Waals forces and neutral hydrogen bonding are the keystone interactions that often drive molecular association. Selected examples of lipid and transmembrane protein association systems are described to illustrate how the association thermodynamics and kinetics are dominated by these keystone noncovalent interactions.
Collapse
Affiliation(s)
- Roger G Hanshaw
- Department of Chemistry and Biochemistry and Walther Cancer Center, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | | | | |
Collapse
|
18
|
Bocharov EV, Mineev KS, Volynsky PE, Ermolyuk YS, Tkach EN, Sobol AG, Chupin VV, Kirpichnikov MP, Efremov RG, Arseniev AS. Spatial Structure of the Dimeric Transmembrane Domain of the Growth Factor Receptor ErbB2 Presumably Corresponding to the Receptor Active State. J Biol Chem 2008; 283:6950-6. [DOI: 10.1074/jbc.m709202200] [Citation(s) in RCA: 172] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|
19
|
Beevers AJ, Kukol A. Transmembrane protein models based on high-throughput molecular dynamics simulations with experimental constraints. Methods Mol Biol 2008; 443:213-227. [PMID: 18446290 DOI: 10.1007/978-1-59745-177-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Elucidating the structure of transmembrane proteins domains with high-resolution methods is a difficult and sometimes impossible task. Here, we explain the method of combining a limited amount of experimental data with automated high-throughput molecular dynamics (MD) simulations of alpha-helical transmembrane bundles in an explicit lipid bilayer/water environment. The procedure uses a systematic conformational search of the helix rotation with experimentally constrained MDs simulations. The experimentally determined helix tilt and rotational angle of a labeled residue with site-specific infrared dichroism allows us to select a unique high-resolution model from a number of possible energy minima encountered in the systematic conformational search.
Collapse
Affiliation(s)
- Andrew J Beevers
- Department of Biological Sciences, University of Warwick, Coventry, UK
| | | |
Collapse
|
20
|
Beevers AJ, Kukol A. Phospholemman Transmembrane Structure Reveals Potential Interactions with Na+/K+-ATPase. J Biol Chem 2007; 282:32742-8. [PMID: 17698851 DOI: 10.1074/jbc.m703676200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phospholemman (PLM) is a 72-residue bitopic cardiac transmembrane protein, which acts as a modulator of the Na(+)/K(+)-ATPase and the Na(+)/Ca(2+) exchanger and possibly forms taurine channels in nonheart tissue. This work presents a high resolution structural model obtained from a combination of site-specific infrared spectroscopy and experimentally constrained high throughput molecular dynamics (MD) simulations. Altogether, 37 experimental constraints, including nine long range orientational constraints, have been used during MD simulations in an explicit lipid bilayer/water system. The resulting tetrameric alpha-helical bundle has an average helix tilt of 7.3 degrees and a crossing angle close to 0 degrees . It does not reveal a hydrophilic pore, but instead strong interactions between various residues occlude any pore. The helix-helix packing is unusual, with Gly(19) and Gly(20) pointing to the outside of the helical bundle, facilitating potential interaction with other transmembrane proteins, thus providing a structural basis for the modulatory effect of PLM on the Na(+)/K(+)-ATPase. A two-stage model of interaction between PLM and the Na(+)/K(+)-ATPase is discussed involving PLM-ATPase interaction and subsequent formation of an unstable PLM trimer, which readily interacts with surrounding ATPase molecules. Further unconstrained MD simulations identified other packing models of PLM, one of which could potentially undergo a conformational transition to an open pore.
Collapse
Affiliation(s)
- Andrew J Beevers
- Department of Chemistry, University of Warwick, Coventry, United Kingdom
| | | |
Collapse
|
21
|
|